Hydrogen gas (H-2) is considered as a signaling molecule and plays multiple roles in plant growth. However, the effect of H-2 on postharvest physiology in lily scales during storage has not been reported. In this study, the regulatory roles of hydrogen-rich water (HRW, a H-2 donor, a concentration of 0.45 mM for 100% HRW) in water status, ion balance, and nutrients in Lanzhou lily (Lilium davidii var. unicolor) scales were investigated. The scales were soaked in HRW for 12 d, and sampling was performed every 3 d for a total of 5 times. The results show that HRW (0, 10, 50, and 100%) increased the fresh weight, dry weight, relative water content, and water loss rate in lily scales, with maximum biological response at 50% HRW. Treatment with 50% HRW significantly increased the K+ content and K+/Na+ ratio in lily scales and decreased Na+ content. The Na+ K+-ATPase, and PM H+-ATPase activities were also increased by 50% HRW treatment. Meanwhile, 50% HRW up-regulated the expression of AKT1 and HA3 genes and down-regulated the expression of NHX2 and SOS1 genes. In addition, 50% HRW treatment significantly increased the expression level of PIP1;5, PIP2A, TIP1;3, and TIP2;2 genes. Treatment with 50% HRW significantly increased the content of water-soluble carbohydrate, sucrose, glucose, and fructose in lily scales, and decreased the content of starch. In addition, 50% HRW treatment significantly increased the activity of alpha-amylase, beta-amylase, total amylase, sucrose synthase, and sucrose phosphate synthase. Collectively, H-2 might enhance the water retention capacity and nutrient content in lily scales by maintaining ion balance, regulating aquaporin, and increasing sugar-metabolizing enzyme activity, thereby prolonging the storage period of postharvest scales of Lanzhou lily.